Comments (14)
I checked the pynco dependencies, they don't include gsl.
pynco
does not but nco
does and pynco
depends on that.
Can you send me the results of your conda info
, conda list
for that env and cat ~/.condarc
?
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Hi, thanks for fast response, yes, here is my conda info
(testpynco) vpn-nsidc227-dhcp:~ brodzik$ conda info
Current conda install:
platform : osx-64
conda version : 4.3.22
conda is private : False
conda-env version : 4.3.22
conda-build version : not installed
python version : 2.7.12.final.0
requests version : 2.18.1
root environment : /opt/miniconda (read only)
default environment : /Users/brodzik/.conda/envs/testpynco
envs directories : /Users/brodzik/.conda/envs
/opt/miniconda/envs
package cache : /opt/miniconda/pkgs
/Users/brodzik/.conda/pkgs
channel URLs : https://conda.anaconda.org/nsidc/channel/main/osx-64
https://conda.anaconda.org/nsidc/channel/main/noarch
https://conda.anaconda.org/nsidc/channel/dev/osx-64
https://conda.anaconda.org/nsidc/channel/dev/noarch
https://conda.anaconda.org/conda-forge/channel/main/osx-64
https://conda.anaconda.org/conda-forge/channel/main/noarch
https://repo.continuum.io/pkgs/free/osx-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/osx-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/osx-64
https://repo.continuum.io/pkgs/pro/noarch
config file : /Users/brodzik/.condarc
netrc file : None
offline mode : False
user-agent : conda/4.3.22 requests/2.18.1 CPython/2.7.12 Darwin/16.7.0 OSX/10.12.6
UID:GID : 13159:200
(testpynco) vpn-nsidc227-dhcp:~ brodzik$
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and my conda list:
(testpynco) vpn-nsidc227-dhcp:~ brodzik$ conda list
# packages in environment at /Users/brodzik/.conda/envs/testpynco:
#
ca-certificates 2017.7.27.1 0 conda-forge/channel/main
certifi 2017.7.27.1 py36_0 conda-forge/channel/main
curl 7.54.1 0 conda-forge/channel/main
esmf 7.0.0 6 conda-forge/channel/main
expat 2.2.1 0 conda-forge/channel/main
gsl 2.1 2 conda-forge/channel/main
h5py 2.7.1 py36_1 conda-forge/channel/main
hdf4 4.2.12 0 conda-forge/channel/main
hdf5 1.8.18 0 conda-forge/channel/main
jpeg 9b 1 conda-forge/channel/main
krb5 1.14.2 0 conda-forge/channel/main
libgcc 4.8.5 1 defaults
libgfortran 3.0.0 0 conda-forge/channel/main
libnetcdf 4.4.1.1 5 conda-forge/channel/main
libssh2 1.8.0 1 conda-forge/channel/main
mkl 2017.0.3 0 defaults
mpich 3.2 5 conda-forge/channel/main
nco 4.6.9 0 conda-forge/channel/main
ncurses 5.9 10 conda-forge/channel/main
netcdf-fortran 4.4.4 3 conda-forge/channel/main
netcdf4 1.3.0 py36_0 conda-forge/channel/main
numpy 1.13.1 py36_0 defaults
openblas 0.2.19 2 conda-forge/channel/main
openssl 1.0.2l 0 conda-forge/channel/main
pip 9.0.1 py36_0 conda-forge/channel/main
pynco 0.0.3 py36_0 conda-forge/channel/main
python 3.6.2 0 conda-forge/channel/main
python-dateutil 2.6.1 py36_0 conda-forge/channel/main
readline 6.2 0 conda-forge/channel/main
scipy 0.19.1 np113py36_0 defaults
setuptools 36.3.0 py36_0 conda-forge/channel/main
six 1.11.0 py36_1 conda-forge/channel/main
sqlite 3.13.0 1 conda-forge/channel/main
tk 8.5.19 2 conda-forge/channel/main
udunits2 2.2.23 1 conda-forge/channel/main
wheel 0.30.0 py_1 conda-forge/channel/main
xz 5.2.3 0 conda-forge/channel/main
zlib 1.2.11 0 conda-forge/channel/main
(testpynco) vpn-nsidc227-dhcp:~ brodzik$
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and my .condarc:
(testpynco) vpn-nsidc227-dhcp:~ brodzik$ more ~/.condarc
channels:
- https://conda.anaconda.org/nsidc/channel/main
- https://conda.anaconda.org/nsidc/channel/dev
- https://conda.anaconda.org/conda-forge/channel/main
- defaults
always_yes: 'True'
show_channel_urls: 'True'
(testpynco) vpn-nsidc227-dhcp:~ brodzik$
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(is there some way to do better block quotes in github markdown?)
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You are using 3 channels and two are on top of conda-forge, that may be the source of the issue.
However, I do not see any package from those channels installed in the env :-/
Note that gsl
was installed, 6th line on your conda list
result, but that is not the right version.
I'll try to inspect the package and see why that happened, meanwhile can you try force conda install gsl=2.2.1
there and see if it fixes the issue?
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(is there some way to do better block quotes in github markdown?)
I usually use gist links to for large outputs, or even attached files.
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Yes, the extra channels are for the packages we deploy from NSIDC--Nothing's installed from there for this example because I was trying to isolate the issue.
In the testgdal env, if I do:
conda install gsl=2.2
it installed gsl and also upgraded scipy and numpy to [blas-openblas]:
gsl: 2.1-2 conda-forge/channel/main --> 2.2.1-blas_openblas_2 conda-for\
ge/channel/main [blas_openblas]
numpy: 1.13.1-py36_0 defaults --> 1.13.1-py36_blas_openblas_200 conda-for\
ge/channel/main [blas_openblas]
scipy: 0.19.1-np113py36_0 defaults --> 0.19.1-py36_blas_openblas_202 conda-for\
ge/channel/main [blas_openblas]
after that I was able to run ncks without the error.
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after that I was able to run ncks without the error.
Cool! I'll close this and conda-forge/nco-feedstock#44 should fix it for good.
Thanks for the report!
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And in my package, will it mean I have to pin gsl? or nco? or pynco? in my package? Right now I just have pynco pinned to <=0.0.3,<0.1.0, but I don't know whether this the correct way to do this.
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You can 'watch' the repo to know when the PR is merged and then click on the CIs build job for the platform you are interested.
It should be up latet today or early tomorrow though.
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Thanks and I see you just merged it. I really appreciate your help and
willingness to explain.
No problem. As soon as https://travis-ci.org/conda-forge/nco-feedstock/builds/281040065 finishes the OS X package will be available. (The Linux package is already in the channel.)
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